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Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images
Dan Ciresan · Alessandro Giusti · luca Maria Gambardella · Jürgen Schmidhuber

Mon Dec 03 07:00 PM -- 12:00 AM (PST) @ Harrah’s Special Events Center 2nd Floor #None
We address a central problem of neuroanatomy, namely, the automatic segmentation of neuronal structures depicted in stacks of electron microscopy (EM) images. This is necessary to efficiently map 3D brain structure and connectivity. To segment {\em biological} neuron membranes, we use a special type of deep {\em artificial} neural network as a pixel classifier. The label of each pixel (membrane or non-membrane) is predicted from raw pixel values in a square window centered on it. The input layer maps each window pixel to a neuron. It is followed by a succession of convolutional and max-pooling layers which preserve 2D information and extract features with increasing levels of abstraction. The output layer produces a calibrated probability for each class. The classifier is trained by plain gradient descent on a $512 \times 512 \times 30$ stack with known ground truth, and tested on a stack of the same size (ground truth unknown to the authors) by the organizers of the ISBI 2012 EM Segmentation Challenge. Even without problem-specific post-processing, our approach outperforms competing techniques by a large margin in all three considered metrics, i.e. \emph{rand error}, \emph{warping error} and \emph{pixel error}. For pixel error, our approach is the only one outperforming a second human observer.

Author Information

Dan Ciresan (IDSIA)
Alessandro Giusti (IDSIA)
luca Maria Gambardella (IDSIA)
Jürgen Schmidhuber (Swiss AI Lab, IDSIA (USI & SUPSI) - NNAISENSE)

Since age 15, his main goal has been to build an Artificial Intelligence smarter than himself, then retire. The Deep Learning Artificial Neural Networks developed since 1991 by his research groups have revolutionised handwriting recognition, speech recognition, machine translation, image captioning, and are now available to billions of users through Google, Microsoft, IBM, Baidu, and many other companies (DeepMind also was heavily influenced by his lab). His team's Deep Learners were the first to win object detection and image segmentation contests, and achieved the world's first superhuman visual classification results, winning nine international competitions in machine learning & pattern recognition. His formal theory of fun & creativity & curiosity explains art, science, music, and humor. He has published 333 papers, earned 7 best paper/best video awards, the 2013 Helmholtz Award of the International Neural Networks Society, and the 2016 IEEE Neural Networks Pioneer Award. He is also president of NNAISENSE, which aims at building the first practical general purpose AI.

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